Amino acid chemistry

Amino acids are the building blocks of proteins and serve many other functions in living organisms. The prime function of DNA is to carry the information needed to direct the proper sequential insertion of amino acids into protein chain during protein synthesis (translation ).

An amino acid is a molecule that contains a terminal acidic carboxyl group (COOH) and a terminal basic amino group (NH₂). The approximately 20 amino acids (plus a few derivatives) that have been identified as protein constituents are alpha-amino acids in which the -NH₂ group is attached to the alpha-carbon next to the -COOH group. Thus, their basic structure is NH₂CHRCOOH, where R is a side chain. This side chain, which uniquely characterizes each alpha-amino acid, determines the molecules overall size, shape, chemical reactivity, and charge. There are hundreds of alpha-amino acids, both natural and synthetic.

The amino acids that receive the most attention are the alpha-amino acids that genes are codes for, and that are used to construct proteins. These amino acids include glycine NH₂CH₂COOH, alanine CH₃CH (NH₂) COOH, valine (CH₃)2CHCH (NH₂)COOH, leucine (CH₃)₂CHCH₂CH(NH₂)COOH, isoleucine CH₃CH₂CH(CH₃)CH(NH₂)COOH, methionine CH₃SCH₂CH₂CH(NH₂)COOH, phenylalanine C₆H₅CH₂CH(CH₂)COOH, proline C₄H₈NCOOH, serine HOCH₂CH(NH₂)COOH, threonine CH₃CH(OH)CH(NH₂)COOH, cysteine HSCH₂CH(NH₂)COOH, asparagine, glutamine H₂NC(O)(CH₂)2CH(NH₂)COOH, tyrosine C₆H₄OHCH₂CHNH₂COOH, tryptophan C₈H₆NCH₂CHNH₂COOH, aspartate COOHCH₂CH(NH₂)COOH, glutamate COOH(CH₂)2CH(NH₂)COOH, histidine HOOCCH(NH₂)CH₂C₃H₃H₂, lysine NH₂(CH₂)₄CH(NH₂)COOH, and arginine (NH₂)C(NH)HNCH₂CH₂CH₂CH(NH₂)COOH.

Proteins are one of the most common types of molecules in living matter. There are countless members of this class of molecules. They have many functions from composing cell structure to enabling cell-to-cell communication. One thing that all proteins have in common is that they are composed of amino acids.

Proteins consist of long chains of amino acids connected by peptide linkages (-CO·NH-). A protein's primary structure refers to the sequence of amino acids in the molecule. The protein's secondary structure is the fixed arrangement of amino acids that results from interactions of amide linkages that are close to each other in the protein chain. The secondary structure is strongly influenced by the nature of the side chains, which tend to force the protein molecule into specific twists and kinks. Side chains also contribute to the protein's tertiary structure, i.e., the way the protein chain is twisted and folded. The twists and folds in the protein chain result from the attractive forces between amino acid side chains that are widely separated from each other within the chain. Some proteins are composed of two of more chains of amino acids. In these cases, each chain is referred to as a subunit. The subunits can be structurally the same, but in many cases differ. The protein's quaternary structure refers to the spatial arrangement of the subunits of the protein, and describes how the subunits pack together to create the overall structure of the protein.

Even small changes in the primary structure of a protein may have a large effect on that protein's properties. Even a single misplaced amino acid can alter the protein's function. This situation occurs in certain genetic diseases such as sickle-cell anemia. In that disease, a single glutamic acid molecule has been replaced by a valine molecule in one of the chains of the hemoglobin molecule, the protein that carries oxygen in red blood cells and gives them their characteristic color. This seemingly small error causes the hemoglobin molecule to be misshapen and the red blood cells to be deformed. Such red blood cells cannot distribute oxygen properly, do not live as long as normal blood cells, and may cause blockages in small blood vessels.

Enzymes are large protein molecules that catalyze a broad spectrum of biochemical reactions. If even one amino acid in the enzyme is changed, the enzyme may lose its catalytic activity.

The amino acid sequence in a particular protein is determined by the protein's genetic code . The genetic code resides in specific lengths (called genes) of the polymer doxyribonucleic acid (DNA), which is made up of from 3000 to several million nucleotide units, including the nitrogeneous bases: adenine, guanine, cytosine, and thymine. Although there are only four nitrogenous bases in DNA, the order in which they appear transmits a great deal of information. Starting at one end of the gene , the genetic code is read three nucleotides at a time. Each triplet set of nucleotides corresponds to a specific amino acid.

Occasionally there an error, or mutation, may occur in the genetic code. This mutation may correspond to the substitution of one nucleotide for another or to the deletion of a nucleotide. In the case of a substitution, the result may be that the wrong amino acid is used to build the protein. Such a mistake, as demonstrated by sickle cell anemia, may have grave consequences. In the case of a deletion, the protein may be lose its functionality or may be completely missing.

Amino acids are also the core construction materials for neurotransmitters and hormones. Neurotransmitters are chemicals that allow nerve cells to communicate with one another and to convey information through the nervous system. Hormones also serve a communication purpose. These chemicals are produced by glands and trigger metabolic processes throughout the body. Plants also produce hormones.

Important neurotransmitters that are created from amino acids include serotonin and gamma-aminobutyric acid. Serotonin(C₁₀H₁₂N₂O) is manufactured from tryptophan, and gamma-aminobutyric acid (H₂N(CH₂)₃COOH) is made from glutamic acid. Hormones that require amino acids for starting materials include thyroxine (the hormone produced by the thyroid gland), and auxin (a hormone produced by plants). Thyroxine is made from tyrosine, and auxin is constructed from tryptophan.

A class of chemicals important for both neurotransmitter and hormone construction are the catecholamines. The amino acids tyrosine and phenylalanine are the building materials for catecholamines, which are used as source material for both neurotransmitters and for hormones.

Amino acids also play a central role in the immune system . Allergic reactions involve the release of histamine , a chemical that triggers inflammation and swelling. Histamine is a close chemical cousin to the amino acid histidine, from which it is manufactured.

Melatonin, the chemical that helps regulate sleep cycles, and melanin, the one that determines the color of the skin, are both based on amino acids. Although the names are similar, the activities and component parts of these compounds are quite different. Melatonin uses tryptophan as its main building block, and melanin is formed from tyrosine. An individual's melanin production depends both on genetic and environmental factors.

Proteins in the diet contain amino acids that are used within the body to construct new proteins. Although the body also has the ability to manufacture certain amino acids, other amino acids cannot be manufactured in the body and must be gained through diet. Such amino acids are called the essential dietary amino acids, and include arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Foods such as meat, fish, and poultry contain all of the essential dietary amino acids. Foods such as fruits, vegetables, grains, and beans contain protein, but they may lack one or more of the essential dietary amino acids. However, they do not all lack the same essential dietary amino acid. For example, corn lacks lysine and tryptophan, but these amino acids can be found in soy beans. Therefore, vegetarians can meet their dietary needs for amino acids as long by eating a variety of foods.

Amino acids are not stockpiled in the body, so it is necessary to obtain a constant supply through diet. A well-balanced diet delivers more protein than most people need. In fact, amino acid and protein supplements are unnecessary for most people, including athletes and other very active individuals. If more amino acids are consumed than the body needs, they will be converted to fat or metabolized and excreted in the urine.

However, it is vital that all essential amino acids be present in the diet if an organism is to remain healthy. Nearly all proteins in the body require all of the essential amino acids in their synthesis. If even one amino acid is missing, the protein cannot be constructed. In cases in which there is an ongoing deficiency of one or more essential amino acids, an individual may develop a condition known as kwashiorkor, which is characterized by severe weight loss, stunted growth, and swelling in the body's tissues. The situation is made even more grave because the intestines lose their ability to extract nutrients from whatever food is consumed. Children are more strongly affected by kwashiorkor than adults because they are still growing and their protein requirements are higher. Kwashiorkor often accompanies conditions of famine and starvation.

See also Bacterial growth and division; Biochemistry; Cell cycle (eukaryotic), genetic regulation of; Cell cycle (prokaryotic), genetic regulation of; Cell cycle and cell division; Chromosomes, eukaryotic; Chromosomes, prokaryotic; DNA (Deoxyribonucleic acid); Enzymes; Genetic regulation of eukaryotic cells; Genetic regulation of prokaryotic cells; Genotype and phenotype; Molecular biology and molecular genetics